Clarity of local vs global indices

[landinjm]

I've been rather inconsistent in naming certain variables based on whether they are some local indexing scheme and the global ones.

For most cases, this is clear when looking at the context, but a few cases are not. Fix either the function comments or the variable names.

[landinjm]

Something that might worth implementing the same as this is strong types

[landinjm]

This has become rather messy with the inclusion of MGInfo, so it's important to fix